AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0720280


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0720280 MtrunA17_Chr5g0410931 100.000 136 0 0 1 136 1 136 3.79e-96 272
Msa0720280 MtrunA17_Chr5g0410951 100.000 136 0 0 1 136 1 136 3.79e-96 272
Msa0720280 MtrunA17_Chr8g0383851 100.000 136 0 0 1 136 1 136 3.79e-96 272
Msa0720280 MtrunA17_Chr8g0383781 100.000 136 0 0 1 136 1 136 3.79e-96 272
Msa0720280 MtrunA17_Chr8g0390361 100.000 136 0 0 1 136 1 136 3.79e-96 272
Msa0720280 MtrunA17_Chr2g0295191 100.000 136 0 0 1 136 1 136 3.79e-96 272
Msa0720280 MtrunA17_Chr7g0237661 100.000 136 0 0 1 136 1 136 3.79e-96 272
Msa0720280 MtrunA17_Chr4g0033041 100.000 136 0 0 1 136 1 136 3.79e-96 272
Msa0720280 MtrunA17_Chr7g0218971 100.000 136 0 0 1 136 1 136 3.79e-96 272
Msa0720280 MtrunA17_Chr4g0046301 100.000 136 0 0 1 136 1 136 3.79e-96 272
Msa0720280 MtrunA17_Chr8g0364801 100.000 136 0 0 1 136 1 136 3.79e-96 272
Msa0720280 MtrunA17_Chr4g0054161 97.059 136 4 0 1 136 1 136 2.60e-93 265
Msa0720280 MtrunA17_Chr8g0363741 97.059 136 4 0 1 136 1 136 2.60e-93 265
Msa0720280 MtrunA17_Chr1g0156021 97.059 136 4 0 1 136 1 136 2.60e-93 265
Msa0720280 MtrunA17_Chr4g0054151 97.059 136 4 0 1 136 4 139 2.61e-93 265
Msa0720280 MtrunA17_Chr8g0388121 96.324 136 5 0 1 136 1 136 1.09e-92 264
Msa0720280 MtrunA17_Chr2g0319141 89.706 136 14 0 1 136 1 136 1.10e-86 248
Msa0720280 MtrunA17_Chr2g0319151 89.706 136 14 0 1 136 1 136 1.10e-86 248
Msa0720280 MtrunA17_Chr2g0319131 85.616 146 11 1 1 136 1 146 1.38e-82 238
Msa0720280 MtrunA17_Chr2g0319121 84.559 136 19 2 1 135 1 135 5.82e-75 219
Msa0720280 MtrunA17_Chr7g0218961 86.607 112 15 0 25 136 2 113 8.01e-66 195
Msa0720280 MtrunA17_Chr7g0222991 67.164 134 43 1 1 134 10 142 5.47e-56 171
Msa0720280 MtrunA17_Chr5g0407311 67.241 116 35 2 1 116 1 113 1.29e-45 144
Msa0720280 MtrunA17_Chr7g0223001 58.647 133 41 3 3 134 27 146 5.46e-43 139
Msa0720280 MtrunA17_Chr7g0240791 100.000 66 0 0 1 66 1 66 9.61e-41 133
Msa0720280 MtrunA17_Chr8g0347231 55.102 98 43 1 37 133 28 125 3.80e-30 105
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0720280 AT1G09200.1 99.265 136 1 0 1 136 1 136 1.62e-95 271
Msa0720280 AT5G65360.1 99.265 136 1 0 1 136 1 136 1.62e-95 271
Msa0720280 AT5G10390.1 99.265 136 1 0 1 136 1 136 1.62e-95 271
Msa0720280 AT5G10400.1 99.265 136 1 0 1 136 1 136 1.62e-95 271
Msa0720280 AT3G27360.1 99.265 136 1 0 1 136 1 136 1.62e-95 271
Msa0720280 AT4G40030.3 97.059 136 4 0 1 136 1 136 3.59e-93 265
Msa0720280 AT4G40030.1 97.059 136 4 0 1 136 1 136 3.59e-93 265
Msa0720280 AT4G40030.4 97.059 136 4 0 1 136 1 136 3.59e-93 265
Msa0720280 AT5G10980.1 97.059 136 4 0 1 136 1 136 3.59e-93 265
Msa0720280 AT4G40040.2 97.059 136 4 0 1 136 1 136 3.59e-93 265
Msa0720280 AT4G40040.3 97.059 136 4 0 1 136 1 136 3.59e-93 265
Msa0720280 AT4G40040.1 97.059 136 4 0 1 136 1 136 3.59e-93 265
Msa0720280 AT4G40030.2 97.059 136 4 0 1 136 29 164 7.05e-93 266
Msa0720280 AT5G65350.1 94.853 136 7 0 1 136 1 136 5.30e-91 260
Msa0720280 AT1G75600.1 93.382 136 9 0 1 136 1 136 1.25e-89 256
Msa0720280 AT1G13370.1 93.382 136 9 0 1 136 1 136 5.55e-89 254
Msa0720280 AT1G19890.1 89.781 137 13 1 1 136 1 137 1.07e-83 241
Msa0720280 AT5G12910.1 71.111 135 34 2 1 135 1 130 9.90e-67 198
Msa0720280 AT1G01370.2 53.982 113 49 2 24 134 63 174 2.97e-31 110
Msa0720280 AT1G01370.1 53.982 113 49 2 24 134 63 174 2.97e-31 110
Msa0720280 AT1G01370.4 53.982 113 49 2 24 134 63 174 2.97e-31 110
Msa0720280 AT1G01370.3 53.982 113 49 2 24 134 63 174 2.97e-31 110

Find 37 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGGTTGCCGGAGCAGATTTC+CGG 0.243304 5_1:-16217173 None:intergenic
TTGGTGGCTAGCTGCTTTCT+TGG 0.277587 5_1:-16217144 None:intergenic
TCACGAAGTGCAACGGTTCC+TGG 0.291776 5_1:-16217225 None:intergenic
TTCTTGACTCCTCCGGTTGC+CGG 0.293014 5_1:-16217186 None:intergenic
TGAGAAGCTCAGTGCTCTTC+TGG 0.304985 5_1:-16217260 None:intergenic
GCTGCTGAAGCTTATCTTGT+TGG 0.357332 5_1:+16217381 Msa0720280:CDS
AGCAGATTTCCGGGCAGCTT+TGG 0.390197 5_1:-16217163 None:intergenic
CGGAAATCTGCTCCGGCAAC+CGG 0.392471 5_1:+16217174 Msa0720280:CDS
GGTTGCCGGAGCAGATTTCC+GGG 0.407337 5_1:-16217172 None:intergenic
CTTTCTTGGTGCCTTTCCTC+CGG 0.425692 5_1:-16217130 None:intergenic
TTATCTTGTTGGTTTGTTTG+AGG 0.428809 5_1:+16217392 Msa0720280:CDS
CGATTTCACGAACAAGTCTC+TGG 0.432729 5_1:-16217299 None:intergenic
AAACAGCGCTGCTTTGAAAT+CGG 0.457546 5_1:-16217344 None:intergenic
AGATTTCCGGGCAGCTTTGG+TGG 0.468887 5_1:-16217160 None:intergenic
AGCTAGCCACCAAAGCTGCC+CGG 0.491500 5_1:+16217154 Msa0720280:CDS
CGAGCAAGTTGAATATCCTT+AGG 0.499677 5_1:-16217459 None:intergenic
GTGTGGCTTCTTGACTCCTC+CGG 0.501667 5_1:-16217193 None:intergenic
AGCTGCCCGGAAATCTGCTC+CGG 0.505877 5_1:+16217167 Msa0720280:CDS
AGTAACTCTCTTAGCATGAA+TGG 0.521941 5_1:-16217430 None:intergenic
AGAGCACTGAGCTTCTCATA+AGG 0.531497 5_1:+16217265 Msa0720280:CDS
TCGCAAATCCACCGGAGGAA+AGG 0.532804 5_1:+16217119 Msa0720280:CDS
TGTTTGCTTTGTACGAGCCA+TGG 0.537743 5_1:-16217094 None:intergenic
GAGAGTTACTATCATGCCTA+AGG 0.550012 5_1:+16217443 Msa0720280:CDS
ACTTGTTCGTGAAATCGCTC+AGG 0.551065 5_1:+16217305 Msa0720280:CDS
TCTTGGTGCCTTTCCTCCGG+TGG 0.556160 5_1:-16217127 None:intergenic
CAGTGCTCTTCTGGTACTTG+CGG 0.579006 5_1:-16217251 None:intergenic
CAAACAGCTCGCAAATCCAC+CGG 0.586123 5_1:+16217111 Msa0720280:CDS
TCACGAACAAGTCTCTGGAA+TGG 0.590006 5_1:-16217294 None:intergenic
CAACTTGCTCGCAGAATCAG+AGG 0.592233 5_1:+16217471 Msa0720280:CDS
AAATCTGCTCCGGCAACCGG+AGG 0.607496 5_1:+16217177 Msa0720280:CDS
TCGCAGAATCAGAGGCGAGA+GGG 0.615698 5_1:+16217479 Msa0720280:CDS
CTCGCAGAATCAGAGGCGAG+AGG 0.629911 5_1:+16217478 Msa0720280:CDS
AAGCCACACAGATTCCGTCC+AGG 0.632383 5_1:+16217207 Msa0720280:CDS
GCGGATCTCACGAAGTGCAA+CGG 0.633057 5_1:-16217232 None:intergenic
GAAGTGCAACGGTTCCTGGA+CGG 0.655834 5_1:-16217221 None:intergenic
GTTCCTGGACGGAATCTGTG+TGG 0.669194 5_1:-16217210 None:intergenic
ACAGCTCGCAAATCCACCGG+AGG 0.704783 5_1:+16217114 Msa0720280:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATCTTGTTGGTTTGTTTG+AGG + chr5_1:16217392-16217411 Msa0720280:CDS 30.0%
AGTAACTCTCTTAGCATGAA+TGG - chr5_1:16217433-16217452 None:intergenic 35.0%
!! AAACAGCGCTGCTTTGAAAT+CGG - chr5_1:16217347-16217366 None:intergenic 40.0%
GAGAGTTACTATCATGCCTA+AGG + chr5_1:16217443-16217462 Msa0720280:CDS 40.0%
! CGAGCAAGTTGAATATCCTT+AGG - chr5_1:16217462-16217481 None:intergenic 40.0%
!! AGAGCACTGAGCTTCTCATA+AGG + chr5_1:16217265-16217284 Msa0720280:CDS 45.0%
! TCACGAACAAGTCTCTGGAA+TGG - chr5_1:16217297-16217316 None:intergenic 45.0%
CGATTTCACGAACAAGTCTC+TGG - chr5_1:16217302-16217321 None:intergenic 45.0%
ACTTGTTCGTGAAATCGCTC+AGG + chr5_1:16217305-16217324 Msa0720280:CDS 45.0%
GCTGCTGAAGCTTATCTTGT+TGG + chr5_1:16217381-16217400 Msa0720280:CDS 45.0%
CAAACAGCTCGCAAATCCAC+CGG + chr5_1:16217111-16217130 Msa0720280:CDS 50.0%
!! CTTTCTTGGTGCCTTTCCTC+CGG - chr5_1:16217133-16217152 None:intergenic 50.0%
! TTGGTGGCTAGCTGCTTTCT+TGG - chr5_1:16217147-16217166 None:intergenic 50.0%
CAGTGCTCTTCTGGTACTTG+CGG - chr5_1:16217254-16217273 None:intergenic 50.0%
TGAGAAGCTCAGTGCTCTTC+TGG - chr5_1:16217263-16217282 None:intergenic 50.0%
! CAACTTGCTCGCAGAATCAG+AGG + chr5_1:16217471-16217490 Msa0720280:CDS 50.0%
TCGCAAATCCACCGGAGGAA+AGG + chr5_1:16217119-16217138 Msa0720280:CDS 55.0%
! AGATTTCCGGGCAGCTTTGG+TGG - chr5_1:16217163-16217182 None:intergenic 55.0%
AGCAGATTTCCGGGCAGCTT+TGG - chr5_1:16217166-16217185 None:intergenic 55.0%
TTCTTGACTCCTCCGGTTGC+CGG - chr5_1:16217189-16217208 None:intergenic 55.0%
GTGTGGCTTCTTGACTCCTC+CGG - chr5_1:16217196-16217215 None:intergenic 55.0%
AAGCCACACAGATTCCGTCC+AGG + chr5_1:16217207-16217226 Msa0720280:CDS 55.0%
GTTCCTGGACGGAATCTGTG+TGG - chr5_1:16217213-16217232 None:intergenic 55.0%
GAAGTGCAACGGTTCCTGGA+CGG - chr5_1:16217224-16217243 None:intergenic 55.0%
TCACGAAGTGCAACGGTTCC+TGG - chr5_1:16217228-16217247 None:intergenic 55.0%
GCGGATCTCACGAAGTGCAA+CGG - chr5_1:16217235-16217254 None:intergenic 55.0%
TCGCAGAATCAGAGGCGAGA+GGG + chr5_1:16217479-16217498 Msa0720280:CDS 55.0%
ACAGCTCGCAAATCCACCGG+AGG + chr5_1:16217114-16217133 Msa0720280:CDS 60.0%
!! TCTTGGTGCCTTTCCTCCGG+TGG - chr5_1:16217130-16217149 None:intergenic 60.0%
AGCTAGCCACCAAAGCTGCC+CGG + chr5_1:16217154-16217173 Msa0720280:CDS 60.0%
AGCTGCCCGGAAATCTGCTC+CGG + chr5_1:16217167-16217186 Msa0720280:CDS 60.0%
GGTTGCCGGAGCAGATTTCC+GGG - chr5_1:16217175-16217194 None:intergenic 60.0%
CGGTTGCCGGAGCAGATTTC+CGG - chr5_1:16217176-16217195 None:intergenic 60.0%
CGGAAATCTGCTCCGGCAAC+CGG + chr5_1:16217174-16217193 Msa0720280:CDS 60.0%
AAATCTGCTCCGGCAACCGG+AGG + chr5_1:16217177-16217196 Msa0720280:CDS 60.0%
CTCGCAGAATCAGAGGCGAG+AGG + chr5_1:16217478-16217497 Msa0720280:CDS 60.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 16217096 16217506 16217096 ID=Msa0720280;Name=Msa0720280
chr5_1 mRNA 16217096 16217506 16217096 ID=Msa0720280-mRNA-1;Parent=Msa0720280;Name=Msa0720280-mRNA-1;_AED=0.47;_eAED=0.47;_QI=0|-1|0|1|-1|1|1|0|136
chr5_1 exon 16217096 16217506 16217096 ID=Msa0720280-mRNA-1:exon:6214;Parent=Msa0720280-mRNA-1
chr5_1 CDS 16217096 16217506 16217096 ID=Msa0720280-mRNA-1:cds;Parent=Msa0720280-mRNA-1
Gene Sequence

>Msa0720280

ATGGCTCGTACAAAGCAAACAGCTCGCAAATCCACCGGAGGAAAGGCACCAAGAAAGCAGCTAGCCACCAAAGCTGCCCGGAAATCTGCTCCGGCAACCGGAGGAGTCAAGAAGCCACACAGATTCCGTCCAGGAACCGTTGCACTTCGTGAGATCCGCAAGTACCAGAAGAGCACTGAGCTTCTCATAAGGAAGCTTCCATTCCAGAGACTTGTTCGTGAAATCGCTCAGGATTTCAAAACAGATCTCCGATTTCAAAGCAGCGCTGTTTCTGCTCTTCAAGAAGCTGCTGAAGCTTATCTTGTTGGTTTGTTTGAGGATACTAATCTCTGTGCCATTCATGCTAAGAGAGTTACTATCATGCCTAAGGATATTCAACTTGCTCGCAGAATCAGAGGCGAGAGGGCTTAG

Protein sequence

>Msa0720280

MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRFRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVSALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA*